JBrowse, VCF-based Variant Track, "Error incorrect header check"

Question

[qizhengyang17]

Hi,

I run JBrowse on my server, and It works fine with FASTA format sequence file and GFF3 format annotation file. But when JBrowse display feature data from VCF files, it gives me this error.

Any help is appreciated. Thanks

[Vitis]

Maybe just as the error said, your VCF has a bad header format? Could you use a different VCF to try it?

[qizhengyang17]

I will try. I can use the vcf file in IGV. When used in JBrowse, the file should be compressed and indexed.

[Vitis]

Can you post your track configuration part for this VCF track?

[qizhengyang17]

[ tracks.HB-10-2 ]
storeClass     = JBrowse/Store/SeqFeature/VCFTabix
urlTemplate    = vcf/HB-10-2_filtered.vcf.gz
category = VCF
type = JBrowse/View/Track/CanvasVariants
key  = SNPs from VCF

[qizhengyang17]

And my VCF header looks like this:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  HB-10-2

[Vitis]

VCF files usually have header lines starting with ## for metadata, reference, etc. Do you have those in your VCF? Something as these:

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
......
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=AF,Number=R,Type=Float,Description="Allelic frequency for alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
......

[qizhengyang17]

yes. I have.

##fileformat=VCFv4.2
##FILTER=<ID=FS,Description="FS > 30.0">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=QD,Description="QD < 2.0">
##FILTER=<ID=SnpCluster,Description="SNPs found in clusters">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
......

##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
##contig=<ID=chr1,length=32081097>
##contig=<ID=chr2,length=53007170>
##contig=<ID=chr3,length=30665222>
##contig=<ID=chr4,length=29345339>
##contig=<ID=chr5,length=49530009>
##contig=<ID=chr6,length=23635499>
##contig=<ID=chr7,length=22269071>
##contig=<ID=chr8,length=21027568>
##contig=<ID=chr9,length=40395599>
##contig=<ID=chrUn,length=43823408>
##reference=file:///home02/qizhengyang/qizhengyang/gatk_rna/genome/HWB.chromosome.fa
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  HB-10-2

[qizhengyang17]

I change my web server from Apache to Nginx, and it works.